The Maltese agricultural sector faces many challenges including lack of organic matter in its soils. The use of organic fertilizers such as cattle or rabbit manure partly addresses this problem. Different doses of manure of rabbit and cattle manure at specific irrigation regimes were used to assess the growth of crops and production of fruit on aubergine and green pepper plants. The overall mean number of green peppers recorded was significantly different than the mean number of aubergine for all four doses of manure applied, using both rabbit and cattle manure, up to an optimum mean number of fruit produced, the optimum being reached at dose 3 for green peppers and dose 4 for aubergines. Additionally, the mean number of fruit was significantly higher when grown in rabbit than in cattle manure. The mean weight of fruit recorded varied significantly between green peppers and aubergines at the highest dose of rabbit manure. When Nitrogen Use Efficiency (NUE) was investigated, the highest nutrient efficiencies were achieved at the higher fertilizer application rates of rabbit manure while for aubergines, the weight increase was not as significant and it may therefore be possible to compromise yield for a better efficiency.